Ruff fixes (#3564)

* fix ruff SIM300 Yoda asserts

ruff ignore ANN101 COM812 NPY002 PTH PLC1901 PLW1514
ruff ignore ANN201 S101 for tests/
rename f->file

* fix ruff F841 local var assigned but never used

* fix ruff SIM113 use enumerate() for index variable

* fix ruff RUF021 parenthesize `a and b` when chaining `and` and `or` together

* fix likely unintentional operator precedence in LobsterEnv._find_relevant_atoms_additional_condition()

(val1 < 0.0 < val2) or (val2 < 0.0 < val1) was not evaluated together

* fix ruff E226 missing whitespace around arithmetic op

* fix super.__init__() call missing parens

* fix ZeroDivisionError in >               self.logger.debug(f"Average time per combi = {(now - start_time) / idx} seconds")

Author: janosh

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.13
+    rev: v0.1.14
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -269,8 +269,8 @@ def get_weights(self, weights_options):
         "+-------------------------------------------------------------+\n"
     )
 
-    with open("ce_pairs.json") as f:
-        ce_pairs = json.load(f)
+    with open("ce_pairs.json") as file:
+        ce_pairs = json.load(file)
     self_weight_max_csms: dict[str, list[float]] = {}
     self_weight_max_csms_per_cn: dict[str, list[float]] = {}
     all_self_max_csms = []

pymatgen/alchemy/filters.py

@@ -265,9 +265,11 @@ def get_sg(s):
 
         for s in self.existing_structures:
             if (
-                self.structure_matcher._comparator.get_hash(structure.composition)
-                == self.structure_matcher._comparator.get_hash(s.composition)
-                and self.symprec is None
+                (
+                    self.structure_matcher._comparator.get_hash(structure.composition)
+                    == self.structure_matcher._comparator.get_hash(s.composition)
+                    and self.symprec is None
+                )
                 or get_sg(s) == get_sg(structure)
             ) and self.structure_matcher.fit(s, structure):
                 return False

pymatgen/analysis/adsorption.py

@@ -582,7 +582,7 @@ def substitute(site, i):
 
         for idx, site in enumerate(sym_slab):
             if dist - range_tol < site.frac_coords[2] < dist + range_tol and (
-                target_species and site.species_string in target_species or not target_species
+                (target_species and site.species_string in target_species) or not target_species
             ):
                 substituted_slabs.append(substitute(site, idx))
 

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -1062,7 +1062,7 @@ def __init__(
         :param max_csm:
         :param symmetry_measure_type:
         """
-        super.__init__(
+        super().__init__(
             self,
             structure_environments,
             additional_condition=additional_condition,

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -1763,10 +1763,8 @@ def get_site_info_for_specie_allces(self, specie, min_fraction=0):
         oxi_state = specie.oxi_state
         for isite, site in enumerate(self.structure):
             if (
-                element in [sp.symbol for sp in site.species]
-                and self.valences == "undefined"
-                or oxi_state == self.valences[isite]
-            ):
+                element in [sp.symbol for sp in site.species] and self.valences == "undefined"
+            ) or oxi_state == self.valences[isite]:
                 if self.coordination_environments[isite] is None:
                     continue
                 for ce_dict in self.coordination_environments[isite]:

pymatgen/analysis/diffraction/tem.py

@@ -20,9 +20,6 @@
 if TYPE_CHECKING:
     from pymatgen.core import Structure
 
-with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json")) as f:
-    ATOMIC_SCATTERING_PARAMS = json.load(f)
-
 __author__ = "Frank Wan, Jason Liang"
 __copyright__ = "Copyright 2020, The Materials Project"
 __version__ = "0.22"
@@ -31,13 +28,18 @@
 __date__ = "03/31/2020"
 
 
+module_dir = os.path.dirname(__file__)
+with open(f"{module_dir}/atomic_scattering_params.json") as file:
+    ATOMIC_SCATTERING_PARAMS = json.load(file)
+
+
 class TEMCalculator(AbstractDiffractionPatternCalculator):
     """
     Computes the TEM pattern of a crystal structure for multiple Laue zones.
     Code partially inspired from XRD calculation implementation. X-ray factor to electron factor
         conversion based on the International Table of Crystallography.
     #TODO: Could add "number of iterations", "magnification", "critical value of beam",
-            "twin direction" for certain materials, "sample thickness", and "excitation error s".
+        "twin direction" for certain materials, "sample thickness", and "excitation error s".
     """
 
     def __init__(

pymatgen/analysis/local_env.py

@@ -1211,9 +1211,9 @@ def __init__(
 
         # Load elemental radii table
         bonds_file = f"{module_dir}/bonds_jmol_ob.yaml"
-        with open(bonds_file) as f:
+        with open(bonds_file) as file:
             yaml = YAML()
-            self.el_radius = yaml.load(f)
+            self.el_radius = yaml.load(file)
 
         # Update any user preference elemental radii
         if el_radius_updates:

pymatgen/analysis/magnetism/heisenberg.py

@@ -146,11 +146,9 @@ def _get_unique_sites(structure):
         unique_site_ids = {}
         wyckoff_ids = {}
 
-        i = 0
-        for indices, symbol in zip(equivalent_indices, wyckoff_symbols):
-            unique_site_ids[tuple(indices)] = i
-            wyckoff_ids[i] = symbol
-            i += 1
+        for idx, (indices, symbol) in enumerate(zip(equivalent_indices, wyckoff_symbols)):
+            unique_site_ids[tuple(indices)] = idx
+            wyckoff_ids[idx] = symbol
             for index in indices:
                 wyckoff[index] = symbol
 

pymatgen/apps/borg/hive.py

@@ -224,7 +224,7 @@ def assimilate(self, path):
             else:
                 for filename in filenames:
                     files = sorted(glob(os.path.join(path, filename + "*")))
-                    if len(files) == 1 or filename in ("INCAR", "POTCAR") or len(files) == 1 and filename == "DYNMAT":
+                    if len(files) == 1 or filename in ("INCAR", "POTCAR") or (len(files) == 1 and filename == "DYNMAT"):
                         files_to_parse[filename] = files[0]
                     elif len(files) > 1:
                         # Since multiple files are ambiguous, we will always